MolNFT v1 · #116024 · protein

Third PDZ domain (PDZ3) of psd-95 complexed with cfmoc-kketev peptide

5D13 · Disks large homolog 4: “Third PDZ domain (PDZ3) of psd-95 complexed with cfmoc-kketev peptide”. X-ray diffraction, 2 ligands (56J, LYS), 6 pockets (best druggability 0.47). MolNFT v1 #116024 on GenesisL1: 3D structure, binding sites…

PDB: 5D13
Type: protein
Length: 425 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Disks large homolog 4; Cfmoc-kketev peptide
UniProt: P31016
Ligands: 56J, LYS
Pockets: 6 · best druggability 0.47

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Disks large homolog 4	protein	100	26% helix, 35% strand	P31016
C	Disks large homolog 4	protein	101	25% helix, 33% strand	P31016
G, E, H, F	Cfmoc-kketev peptide	protein	6	0% helix, 33% strand	—

Ligands and binding sites

56J · 3-(9H-fluoren-9-yl)propanal · ligand · 5 copies · chains B, G, A, E, C, H, D, F
LYS · Lysine · ligand · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.47	0.85	17	empty
2	86	0.39	0.77	14	56J
3	77	0.35	0.75	15	56J
4	67	0.32	0.75	16	56J
5	62	0.32	0.75	14	56J

Interfaces

7 interfaces between chains.

B–G · 489 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 423 Å² buried · 11 hydrogen bonds · protein-protein
C–H · 397 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 383 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 328 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

P31016 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P31016) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P31016
Elsewhere: RCSB PDB 5D13 · PDBe 5D13 · UniProt P31016

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